+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j9f | |||||||||
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タイトル | Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C | |||||||||
要素 |
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キーワード | VIRUS/CELL ADHESION / deglycosylated receptor / picornavirus / PVR / CD155 / enterovirus / cell entry / VIRUS-CELL ADHESION complex | |||||||||
機能・相同性 | 機能・相同性情報 susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / symbiont-mediated suppression of host translation initiation / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / symbiont-mediated suppression of host translation initiation / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / cell adhesion molecule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / adherens junction / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / signaling receptor activity / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular space / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Human poliovirus 1 Mahoney (ポリオウイルス) Homo sapiens (ヒト) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 9 Å | |||||||||
データ登録者 | Strauss, M. / Filman, D.J. / Belnap, D.M. / Cheng, N. / Noel, R.T. / Hogle, J.M. | |||||||||
引用 | ジャーナル: J Virol / 年: 2015 タイトル: Nectin-like interactions between poliovirus and its receptor trigger conformational changes associated with cell entry. 著者: Mike Strauss / David J Filman / David M Belnap / Naiqian Cheng / Roane T Noel / James M Hogle / 要旨: Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to ...Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to form an expanded form of the capsid called the 135S particle. This expansion results in the externalization of the myristoylated capsid protein VP4 and the N-terminal extension of the capsid protein VP1, both of which become inserted into the cell membrane. Structures of the expanded forms of poliovirus and of several related viruses have recently been reported. However, until now, it has been unclear how receptor binding triggers viral expansion at physiological temperature. Here, we report poliovirus in complex with an enzymatically partially deglycosylated form of the 3-domain ectodomain of Pvr at a 4-Å resolution, as determined by cryo-electron microscopy. The interaction of the receptor with the virus in this structure is reminiscent of the interactions of Pvr with its natural ligands. At a low temperature, the receptor induces very few changes in the structure of the virus, with the largest changes occurring within the footprint of the receptor, and in a loop of the internal protein VP4. Changes in the vicinity of the receptor include the displacement of a natural lipid ligand (called "pocket factor"), demonstrating that the loss of this ligand, alone, is not sufficient to induce particle expansion. Finally, analogies with naturally occurring ligand binding in the nectin family suggest which specific structural rearrangements in the virus-receptor complex could help to trigger the irreversible expansion of the capsid. IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into ...IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into three-dimensional experimental maps of the receptor-virus complex. The molecular interactions we see between poliovirus and its receptor are reminiscent of the nectin family, by involving the burying of otherwise-exposed hydrophobic groups. Importantly, poliovirus expansion is regulated by the binding of a lipid molecule within the viral capsid. We show that receptor binding either causes this molecule to be expelled or requires it, but that its loss is not sufficient to trigger irreversible expansion. Based on our model, we propose testable hypotheses to explain how the viral shell becomes destabilized, leading to RNA uncoating. These findings give us a better understanding of how poliovirus has evolved to exploit a natural process of its host to penetrate the membrane barrier. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3j9f.cif.gz | 216.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j9f.ent.gz | 170.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j9f.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 3j9f_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j9f_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 3j9f_validation.xml.gz | 45.5 KB | 表示 | |
CIF形式データ | 3j9f_validation.cif.gz | 66.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j9/3j9f ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9f | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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対称性 | 点対称性: (シェーンフリース記号: I (正20面体型対称)) |
-要素
-タンパク質 , 7種, 7分子 1234789
#1: タンパク質 | 分子量: 33488.613 Da / 分子数: 1 / 断片: UNP residues 580-881 / 由来タイプ: 天然 由来: (天然) Human poliovirus 1 Mahoney (ポリオウイルス) 参照: UniProt: P03300 |
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#2: タンパク質 | 分子量: 30075.783 Da / 分子数: 1 / 断片: UNP residues 70-341 / 由来タイプ: 天然 由来: (天然) Human poliovirus 1 Mahoney (ポリオウイルス) 参照: UniProt: P03300 |
#3: タンパク質 | 分子量: 26547.482 Da / 分子数: 1 / 断片: UNP residues 342-579 / 由来タイプ: 天然 由来: (天然) Human poliovirus 1 Mahoney (ポリオウイルス) 参照: UniProt: P03300 |
#4: タンパク質 | 分子量: 7603.405 Da / 分子数: 1 / 断片: UNP residues 2-69 / 由来タイプ: 天然 由来: (天然) Human poliovirus 1 Mahoney (ポリオウイルス) 参照: UniProt: P03300 |
#5: タンパク質 | 分子量: 12869.564 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P15151 |
#6: タンパク質 | 分子量: 10999.521 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P15151 |
#7: タンパク質 | 分子量: 9952.081 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P15151 |
-糖 , 5種, 7分子
#8: 多糖 | #9: 多糖 | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #10: 多糖 | #11: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #13: 糖 | ChemComp-NAG / | |
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-非ポリマー , 1種, 1分子
#12: 化合物 | ChemComp-PLM / |
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-詳細
非ポリマーの詳細 | GLYCOSYLATION IN THIS ENTRY IS DERIVED FROM STARTING STRUCTURE PDB ENTRY 4FQP AND DOES NOT ...GLYCOSYLAT |
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配列の詳細 | THE RECEPTOR HAS BEEN MODELED AS THREE INDIVIDUAL DOMAINS WITH DUPLICATED, CLASHING LINKER SEGMENTS ...THE RECEPTOR HAS BEEN MODELED AS THREE INDIVIDUAL |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: NO / ホストのカテゴリ: VERTEBRATES / 単離: STRAIN / タイプ: VIRION | ||||||||||||||||||||
天然宿主 | 生物種: Homo sapiens | ||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM200FEG / 日付: 1999年11月1日 |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 120 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / Cs: 2 mm |
試料ホルダ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
撮影 | フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||
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3次元再構成 | 解像度: 9 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 3822 / ピクセルサイズ(公称値): 1.77182 Å / ピクセルサイズ(実測値): 1.77182 Å / 詳細: (Single particle--Applied symmetry: I) / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: RECIPROCAL / 詳細: REFINEMENT PROTOCOL--rigid body | ||||||||||||
原子モデル構築 | PDB-ID: 1HXS | ||||||||||||
精密化ステップ | サイクル: LAST
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